Additional Files Scaffolder Kaether et. al

Additional File 1 auN(A) and Misassemblies as computed by Quast Fig. 1 (Left:) auN, (Middle:) misassemblies and (Right:) auNA as computed by Quast for the new scaffolds produced by AncST. Fig. 2 (Left:) auN, (Middle:) misassemblies and (Right:) auNA as computed by Quast for the new scaffolds produced by ntJoin. Fig. 3 (Left:) auN, (Middle:) misassemblies and (Right:) auNA as computed by Quast for the new scaffolds produced by Ragout2. 1 Fig. 4 (Left:) auN, (Middle:) misassemblies and (Right:) auNA as computed by Quast for the new scaffolds produced by CSAR. Fig. 5 (Left:) auN, (Middle:) misassemblies and (Right:) auNA as computed by Quast for the new scaffolds produced by RagTag. 2 Additional File 2 Coverage of Main Human Chromosomes with Quast Alignments of New Scaffolds Fig. 6 Shown are data based on the results of scaffolding the human genome with at least 5 % rearranged sequence against (left:) chimp and (right:) chimp and bonobo from AncST. Relative coverage (X-axis) of 24 human chromosomes (22+X+Y) (Y-axis) by all alignments produced by Quast. First, the total length of all alignments of a reference chromosome with any new scaffolds is noted. Then each new scaffold is assigned its relative coverage as the proportion of the length of its alignments with the reference. Scaffolds covering at least 50 % of a reference are colored and the rest is gray. Relative coverage by one contig is bordered by white vertical lines. Fig. 7 Shown are data based on the results of scaffolding the human genome with at least 5 % rearranged sequence against (left:) chimp and (right:) chimp and bonobo from ntJoin. Details can be found in caption of 6. 3 Fig. 8 Shown are data based on the results of scaffolding the human genome with at least 5 % rearranged sequence against (left:) chimp and (right:) chimp and bonobo from RagTag. Details can be found in caption of 6. Fig. 9 Shown are data based on the results of scaffolding the human genome with at least 5 % rearranged sequence against (left:) chimp and (right:) chimp and bonobo from CSAR. Details can be found in caption of 6. 4 Fig. 10 Shown are data based on the results of scaffolding the human genome with at least 5 % rearranged sequence against chimp and bonobo from Ragout2. Details can be found in caption of 6. 5 Additional File 3 Drosophila Assemblies Used Table 1 Genomes of Drosophila species used. same in NCBI Ref.(erence) means that the Contig or Scaffold level assembly used as a scaffolding target is also marked as the reference chromosome for this species on NCBI. Accession Species Abbreviation Assembly Level NCBI Ref. Identifier GCA 018904445.1 D. sechellia Dsec Scaffold GCF 004382195.2 A GCA 039725655.1 D. simulans Dsim Contig GCF 016746395.2 B GCA 000778455.1 D. melanogaster Dmel Contig GCF 000001215.4 C GCA 018904385.1 D. yakuba Dyac Contig GCF 016746365.2 D GCA 018904525.1 D. erecta Dere Scaffold GCF 003286155.1 E GCA 018904475.1 D. mauritiana Dmau Scaffold GCF 004382145.1 F GCA 018903625.1 D. teissieri Dtei Contig GCF 016746235.2 G GCA 005876975.1 D. orena Dore Contig same H GCF 018153835.1 D. eugracilis Deug Contig same I GCA 018148935.1 D. biarmipes Dbia Contig GCF 025231255.1 J GCA 018152695.1 D. takahashii Dtak Contig GCF 030179915.1 K GCF 018152265.1 D. ficusphila Dfic Contig same L GCF 018152505.1 D. elegans Dele Contig same M GCF 018152115.1 D. rhopaloa Drho Contig same N GCA 008042655.1 D. burlai Dbur Scaffold same O GCA 018152535.1 D. kikkawai Dkik Contig GCF 030179895.1 P GCA 008042735.1 D. leontia Dleo Scaffold same Q GCA 021223765.1 D. bipectinata Dbip Scaffold GCF 030179905.1 R GCA 018153235.1 D. malerkotliana Dmal Contig same S GCA 018148915.1 D. ananassae Dana Contig same T 6 Additional File 4 Scaffolding Evaluation of Drosophilas Fig. 11 auN as computed by Quast for 20 Drosophila newly scaffolded species. The new scaffolds for computed by RagTag for Drosophila biarmipes (J) show an auN of around 180 million while we set the upper limit of the y-axis to 75 million for clearer display. Identifier correspondence and further details in Table 1. 7 Fig. 12 Number if misassemblies as computed by Quast for the 11 Drosophila newly scaffolded species with a chromosomescale reference genome on NCBI. Further details in Table 1. 8 Additional File 5 Assessment of Reference Chromosome Coverage with New Scaffolds Fig. 13 Shown are all reference chromosomes for the Drosophila biarmipes official reference assembly on NCBI on the y-axis. For each reference chromosome, the upper bar displays results computed with the AncST-based pipeline and the lower bar the ones from RagTag. The bars are stacked according to the coverage of each reference chromosome by new scaffolds from the respective tool. The coverage is estimated by the total alignment length of all minimap alignments recorded in the output of Quast. Only contigs/scaffolds covering at least a third of the total alignment length are drawn colored while the rest is kept gray. Each color represents a different new scaffold which are indicated in the legend. 9 Fig. 26 Left: auNA from Quast for each Drosophila species with a chromosome-level reference as in main text. Right: Same analysis as in main text but using AncST weights for RagTag and ntJoin. 16